RE: They do good I here
Welcome to SS. Are you going to use the truck for just personal use or are you going to use it for any type of money making work?
First for the DL issue. You should not need a CDL even if you are operating commercially. A commercial operator is anyone that uses the truck to make money.
For the title issue. If you get an SF-97 take it to the local SOS office and get a regular title. If you do not have a title or sf-97 you would need to apply for a bonded title. You would also need a vin inspection by a law enforcement officer. I have not heard about the equipment inspection going away but they should only be needed if you are making a vehicle. A bonded title should only need a Vin inspection. They are done on the same form. A form tr-54 if I remember right. If the vehicle is worth under $2500 then no actual bond is needed. If it is worth over $2500 then you would need to pay extra money to get bond when you get the new title.
Lastly registration.
You have two options. One is a declared weight title. This would be your max weight of any thing you are hauling along with the weight of the vehicle. In other words, your vehicle GVWR. On a stock deuce it would be in the area of 24,000 lbs. This would allow you to use the truck for any purpose. You could also get a historical plate but this limits your use to going to parades, shows, weekend rides, etc. It kind of implies you can't haul a load since you would be using it as a truck not a collector's vehicle. The law is kind of vague so you could get away with it once in a while. If you are hauling 10,000 lbs every weekend a LEO might stop you and ticket you as violating the historical plate law.
A third option is a farm plate. You could get by with this but I don't know what the SOS wants you to show to prove you are a farm. If you are more than 150 miles from you house you would need an F endorsement. I am not sure if you would really need one as you would be less than the GVRW that requires a CDL. By getting a farm plate you are also declaring the vehicle is for commercial use on a farm so other restrictions might apply. If you think you are going this route I could check it out for you.
The last issue is shortening the deuce and taking one axle off. If you change the truck that much you would be making a new truck by law. This means that you would have to get an inspection and a state issued vin. The year would change to the year you made it or modified it. This would make it not eligible for a historical plate anymore. This is strict letter of the law. Most of the time you would be OK since most people would not know that you modified the truck. Think the cars with the body of a car on the chassis of a blazer. When you modify a truck this much it is considered a new truck built by you. Some officers in the state know the difference and will impound the vehicle until you get the paperwork straightened out. Do I think you can get by without getting a state issued vin? Probably. Is it legal? No. I have an F-350 that has a rusted out cab. I am putting a rust free cab on it. I will need to get an inspection and a new state issued vin. If I just used the title to the new cab the vin would show an F150 while the chassis is clearly an F-350. This is the kind of stuff crooks do with stolen vehicles. Why not change the vin from my old cab? It is a felony to remove or deface a vin no matter what teh reason. Even if the vehicles are not stolen and you have not criminal intent.
I know we see people selling titles with data plates from time to time. Especially with the Jeep guys. This is technically a felony. Even though our data plates come on and off with a screw driver it does not matter. Jeep guys that change a full tub technically not legal to change the data plate from one to another. The vehicle would be considered a new vehicle built from parts and would need a new vin. Boyd Coddington got in trouble because he was rebuilding vehicles and titling them as say a 1929 ford with an old title. The correct way to title it is as a 1929 replica built in 2008. Most of the time most cops will not know the difference but there are auto theft task forces that do know this stuff and when they find something like an F-150 vin attached to an F-350 they will impound it to check for stolen parts and fine you for not doing things right.
Ok. I am now getting off my soap box. Anyone is free to PM me for any clarification or questions.
If you couple this with air steering, good tires, and a locker you have one nice trail truck that will go allot of places a full size would not think about going. 
